Abstract
Structural characteristics of a central segment of the HIV RNA trans-activation response element (TAR) have been studied in aqueous solution. The investigated segment (TAR-14), comprising nucleotides 26–39 of the wild-type HIV genome (GAGC-CUGGGA-GCUC sequence), forms the TAR apical hairpin with a six-base loop and a stem of 4 base pairs. Raman spectra were recorded in a wide temperature range and the spectral series analyzed by means of factor analysis (FA) and a consequent fit to a thermodynamic model. The model was applied for temperatures above 20°C because of spectroscopic indication of possible intermolecular complexes at lower temperatures. FA results corresponded to a monomolecular reaction of the hairpin opening characterized by a melting temperature of 71°C and ∆G37 = −3.2 kcal/mol. Besides the process of the hairpin opening, the FA revealed also substantial, approximately linear, temperature induced changes of the closed hairpin Raman spectrum. Spectral changes attributed to this effect indicated partial disordering of the A-type duplex geometry of the stem, opening of intraloop hydrogen bonds, weakened conformational regularity of the loop guanosines and release of the loop uracil.